The unfavorable sanitary-epidemiological situation in the conditions of natural disasters and man-made disasters testifies to the need to improve the activities of the sanitary-epidemiological service as one of the most important links in ensuring the safety of the environment for public health. In an emergency situation related to the unfavorable flood situation in the Tuapse district of Krasnodar region in 2012 and 2014, an increase in the incidence of the sum of acute intestinal infections (AII) in the post-flood periods was registered, which exceeded the average long-term morbidity rate by 33.3 % and 20.9 %, respectively. Mostly recorded AII bacterial etiology to 53.8 %, caused by conditionally pathogenic microflora. The peculiarity of the situation was an increase in the population of intestinal infections of viral etiology by 20 times and caused by pathogenic microorganisms by 2 times compared to the preplant period. The share of water factor in the transmission of AII cases was 34.8 % in 2012, 14.7 % in 2014, the leading pathway of infection - contact and household. The implementation of sanitary-hygienic and anti-epidemic measures provided the operational management of the system of life support of the population during the natural disaster.